AD - Ratio Total Energy to Fuel Output Energy

The general answer to why adding a more energy-dense organic increases emissions is because we assume that all inputs cause an output. If coproducts or fuel are not increasing with increased inputs, then emissions must be.

What I suspect you're looking at is just confusing based on the way the model deals with the intermediate calculations. In many cases this calculation may look confusing because between Alt Fuel Prod and Upstream Results we would have broken the total out into NG/Diesel/Electricity/Biomass percents on Energy Use, so multiplying by the total energy later is just bringing things back to non-percent values.

However I'm not sure about your specific question. Could you point out the cell that is causing confusion, because I'm not entirely sure where you're looking based on the description. Thanks.

Yes, changing that on Fuel Char is likely the correct approach.

And I'll reiterate that you need not be too worried about that total energy value showing up. The basic format of most fuels on row 11 is as follows:

[(% of energy as NG) * (NG emis) + (% of energy as diesel) * (diesel emis) + ...] * (total energy)

Where each of the percent terms being of the form

(NG energy) / (total energy)

So overall the total energy just cancels itself out. There's obviously a bit more to the equations, but that's the bulk of it.